ViennaCL: First draft, including all operations for sequential vectors.

Mostly derived from existing CUSP interface.
viennacl.py package for BuildSystem included, detected correctly by BuildSystem,

ViennaCL: First draft, including all operations for sequential vectors.

Mostly derived from existing CUSP interface.
viennacl.py package for BuildSystem included, detected correctly by BuildSystem, but download option untested.
Everything compiles and the standard 'make test' passes. In-depth tests still required.

show more ...

dev: revert master back to dev by resetting PETSC_VERSION_RELEASE
and reverting 408b84210f4204d220c33572b1c41f435c302dbf

cuda/threadcomm: configure print message to use petsc-dev [when using release]

SuperLU_DIST: upgrade to v3.3 @ 2013-04-10

Fixes use of MPI_TAG_UB that caused divide-by-zero with Open MPI.

parmetis: update to parmetis-4.0.2-p4.tar.gz
fixes nightly build src/ksp/ksp/examples/tests/ex31 in examples_next_arch-freebsd-cxx-pkgs-opt_wii.log

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory

Merge branch 'knepley/plex'

Improved support for discretizing PDEs. Cell geometry and FVM. Little to
no topology.

* knepley/plex:
SNES ex12: Fix leak
TS ex11: error if dim != DIM because memory corruption occurs otherwise
DMPlex: All quadrilateral geometry tests working
DMPlex: remove unused variable
DMPlex: Hexahedron geometry tests now pass
DMPlex: More geometry work
DMPlex: use PETSC_HAVE_TGAMMA to get the build working on windows
configure: add test for tgamma() [this is missing on windows]
DMPlex: Added random transform tests for tets - Fixed memory leak
DMPlex: Fixed 3D geometry
DMPlex: FVM geometry tests now work for triangles
DMPlex: one more win32/complex fix
DMPlex: Enhanced geometry tests - Added random transforms of the reference triangle in 2D
DMPlex: Fixed complex problems in geometry calculation
DMPlex: Fixed Fortran test output
DMDT: M_PI --> PETSC_PI
DMPlex: Reorganized geometry testing
TS ex11: Put in 3D inflow and outflow ids from the command line
DMPlex: Added DMPlexRestoreCone/Support() to F90 interface definition header - Also added to test ex1f90
TS ex11: Need to make these ids input from the command line
DMPlex: Add Fortran bindings
DMPlex: Reorder tet output since I order tets differently
Builder: Link Fortran examples with Fortran linker
DMPlex: Fixed leak in example
DMPlex: Tutorial now shows how to output VTK
PetscViewer: Added VTK type for Fortran
DMPlex: Remove parameter names from prototype
DMPlex: Geometry fixes for C++ complex
DMAKKT: Remove from build
DMPlex: Now DMPlexCreateSection() only has an F90 interface
SNES: add Fortran bindings to DMSNESSet{Function,Jacobian}
SNES: remove superfluous casting in DM local Fortran bindings
SNES: compile zdmlocalsnesf.c
DMDT: Fix Fortran wrapper
DMPlex: Added Fortran interface for DMPlexMatSetClosure()
PetscSection: Added docs, enabled Fortran wrappers
DM: Added Fortran bindings for DMSNESSetFunction/JacobianLocal()
SNES ex12: Looks like 3D Neumann conditions are working
DMPlex: Fix volume determination for 2D in 3D
DMPlex: Better error reporting
SNES ex12: Boundary integration seems to work in 2D
DMPlex+FEM: Fix for boundary integration
TS ex11: Better error reporting
DMPlex ex8: Added FVM geometry tests
DMPlex: Fixed FVM geometry for 2D in 3D
SNES ex62: Now using PetscDT quadrature
DMDT: Translated FIAT's Gauss-Jacobi quadrature
DMPlex: Fix geometry tests - Fix tests for 2D projection
DMPlex: Geometry fixes
DMPlex: Small fixes for geometry
DMPlex: Fixed damn prototype
PetscSection: Added VecSetValuesSectionF90() - Fixed bug in Vec Fortran header
DMPlex: Added Fortran defines for additional insert modes
DMPlex: Silence warning in DMPlexInvertCells_Internal()
DMPlex: Functions passed to evaluation routines now return void and pass results in arguments
DMPlex: Now we give an explicit embedding dimension to the FVM geometry methods
DMPlex: Fixed complication with complex - Started to add 3D geometry stuff
TS ex11: Replace edge geometry with call to DMPlexComputeCellGeometryFVM()
DMPlex: Added normal argument to DMPlexComputeCellGeometryFVM() - This is only calculated for faces - Added calculation for faces in 2D
DMPlex: Damn makefiles
DMPlex: Added declaration for DMPlexCreateCGNS()
TS ex11: Reorganized computation of geometry in preparation for 3D
Builder: Now individual tests can have requirements - The key is 'requires', and it takes a list of package names - Also fixed up showSingleRun()
TS ex11: Use new DMPlexComputeCellGeometryFVM()
DMPlex: Added DMPlexComputeCellGeometryFVM() - Added internal volume methods
DMPlex: fix const and int vs. PetscInt
DMPlex: Better error reporting
DMPlex+ExodusII: Fixed reading of quads - Was broken by 2e1b13c25062c3c40593ce7412c5cd227259ade7
DMPlex: Hex cell geometry was broken - I don't see how this test passed before
DMPlex: Regression cleanup
DMPlex: Regression cleanup
SNES ex12: Fixed sign for Neumann BC
DMPlex+FEM: The dimension does not change for boundary elements
DMPlex: Geometry now works for boundary elements
DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals
SNES ex12: Reorganized tests, still working on Neumann conditions - Fixed boundary face label
DMPlex: Turn off CGNS by default
DMPlex: Added 1D cell geometry
DMPlex: DMPlexCreateCGNS()
DMPlex: Updated test ex1 output
DMPlex: Fixed compiler problems with complex
SNES ex12: Now does boundary integration - Still not verifying exact solution for Neumann conditions
DMPlex: Fix DMPlexComputeCellGeometry() to handle lower dimensional cells
DMPlex: Fixed error in projection from 3D to 2D - Need to check for case where normal is already z
DMPlex: Adding boundary integration
DMPlex: Fixed cell inversion for TetGen to commute with mesh interpolation
SNES ex12: Cleaning up ex12 testing
DMPlex: Added integration over boundary to DMPlexComputeResidualFEM() - Added quadBd, f0/1BdFuncs to PetscFEM struct - Needs to be tested
FEM Generation: We now allow a *_bd.h header that holds boundary discreization
Builder: Fixed regression requirements
Builder: Fixed specification of multiple tests to run
DMPlex ex7: Orientations now working properly
DMPlex: Changed orientation convention and fixed many bugs
SNEX ex12: Ignore generated headers
SNEX ex12 and ex52: Remove CTetGen warnings from test output - Fixed this in CTetGen repository
DMPlex: Fix default |J| for DMPlexComputeCellGeometry()
DMPlex: Fix for cell geometry (unbelievable screwup)
DMPlex ex7: Check that |J| is nonzero for each cell in interpolated mesh
DMPlex: Allow DMPlexComputeCellGeometry() to work with interpolated meshes
DMPlex: Added prototype for DMPlexCopyCoordinates(), and docs for that and DMPlexInterpolate()
DMPlex: Added F90 interface for DMPlexComputeCellGeometry()

Conflicts:
include/petscdmplex.h

show more ...

Updating to Elemental version 0.79-p1

Merge branch 'knepley/builder-sharedlibrary-fix'

chaco: update to patched tarball that fixes dot()/norm() namespace conflict with SPAI

nightlybuilds: disable testexamples_DATAFILESPATH for single precision builds.

DMPlex+FEM: Fix for boundary integration

Merge branch 'jed/aijcusparse-icc'

* jed/aijcusparse-icc:
MatSeqAIJCUSPARSE: make private functions static
txpetscgpu: upgrade to version 0.1.0
aijcusparse : fixed MatGetFactor and other small

Merge branch 'jed/aijcusparse-icc'

* jed/aijcusparse-icc:
MatSeqAIJCUSPARSE: make private functions static
txpetscgpu: upgrade to version 0.1.0
aijcusparse : fixed MatGetFactor and other small issues in this class
ksp tests: new tests for ksp algorithms using aijcusparse methods
vscatcusp : fixed compiler warnings
MatSeqAIJCUSPARSE: white space, style issues, static and extern functions
aijcusparse: ICC/Cholesky preconditioners

Conflicts:
src/mat/impls/aij/seq/seqcusparse/aijcusparse.cu (PetscObjectComposeFunction usage)

show more ...

ams: download from git

txpetscgpu: upgrade to version 0.1.0

DMPlex+FEM: Fixed quadrature coordinate handling for boundary integrals

Merge branch 'jed/elemental-0.78-p1'

* jed/elemental-0.78-p1:
Elemental: no support for 64-bit indices so requires32bitint=1
elemental.py: upgrade to 0.78-p1

Merge branch 'jed/superlu-dist-3.3'

* jed/superlu-dist-3.3:
SuperLU_DIST: upgrade to release 3.3
SuperLU_DIST.py: upgrade to pre-release version 3.3

Merge branch 'jed/pkg-download-git'

* jed/pkg-download-git:
SuperLU_DIST: point gitcommit at v3.2
Git download: ML, SuperLU_DIST, MUMPS, ctetgen
package.py: add support for cloning from Git

nightlybuilds: configure missing testexamples_DATAFILESPATH
ref: c37110e4b4503f02823ae381a742b0e6a545e769

Merge branch 'balay/threadcomm-fixes'

* 'balay/threadcomm-fixes'
threadcomm: fix potential "set, but not used variable" warning
threadcomm: fix build on bgl/c++ threadcommred.c
threadcomm: CHK

Merge branch 'balay/threadcomm-fixes'

* 'balay/threadcomm-fixes'
threadcomm: fix potential "set, but not used variable" warning
threadcomm: fix build on bgl/c++ threadcommred.c
threadcomm: CHKERRQ() shouldn't be used on sysctlbyname(). #155945 Fixes on bsd:

show more ...

Merge branch 'jed/pkg-download-git' into jed/superlu-dist-3.3

Merged to obtain Git support for naming the new version of SuperLU_DIST.

* jed/pkg-download-git:
SuperLU_DIST: point gitcommit at v3.

Merge branch 'jed/pkg-download-git' into jed/superlu-dist-3.3

Merged to obtain Git support for naming the new version of SuperLU_DIST.

* jed/pkg-download-git:
SuperLU_DIST: point gitcommit at v3.2
Git download: ML, SuperLU_DIST, MUMPS, ctetgen
package.py: add support for cloning from Git

Conflicts:
config/PETSc/packages/SuperLU_DIST.py

show more ...

SuperLU_DIST: upgrade to release 3.3

Builder: Fixed log files
- Regression now goes in regression.log
- Quadrature generation now goes in quadrature.log

Elemental: no support for 64-bit indices so requires32bitint=1

elemental.py: upgrade to 0.78-p1